Protien Molecules Flashcards
What bonds are amino acids linked by
Covalent bonds in linear chain
Primary structure of proteins
Linear amino acid sequence
Secondary structure of proteins
Polypeptide folding into regular shapes (forms domains)
Tertiary protein structure
Arrangement of one or more domains (3D structure)
Quaternary protein structure
Arrangement of multiple polypeptide chains in one protein - forms protein complex with subunits
What are domains
How elements of secondary structure are packed together
What is the alpha carbon in an amino acid
Linked to amino group (-NH2), a carboxyl group (-COOH), a alpha hydrogen atom and an R group (chiral carbon)
What form do amino acids exist in neutral pH
Zwitterion form at neutral pH
What does the formation of a dipeptide from two amino acids results in
Loss of water - condensation reaction
What is a residue
Each amino acid unit of polypeptide chain called a residue
What structure do peptide bonds adopt
Rigid planar structure
How are disulphide bonds formed
Between side chains of two cysteine residues under oxidising conditions
How can disulphide bonds be cleaved
By reducing agents such as B (beta) - mercaptoe thanol
What are histones composed of
DNA packaging - many Arg, Lys => very basic proteins
What are membrane proteins composed of
Many Leu, Val and ile = > hydrophobic proteins
What amino acids compose extracellular proteins
Many Cys to form disulphide bond, stable protein
What is a result of cis configuration of side chains
Neighbouring amino acids can result in steric hinderance
Types of non covalent bonds
Hydrogen bonds
Salt bridges (electrostatic interaction)
Vẫn đẻr waals interaction
What are Hydrogen bonds essential for
Crucial for protein folding and formation of secondary structure
Formation of salt bridges and their importance
-Formed by attractive forces between oppositely charged atoms
- important in quaternary structure formation
Where do Hydrogen bonds form on secondary structure of protein
Between -Nh and -CO groups on different but adjacent strands
What are the two main secondary structures of a protein
Alpha helixes (a-helices)
Beta sheet (B-sheet)
What are tertiary structures composed of
‘Bundles’ (aka domains) of secondary structures
Characteristics of a domain
-hydrophilic side chains exposed
-hydrophobic side chains buried in hydrophobic core
What is a domain
Region of polypeptide chain that folds independently and self stabilising
How do polypeptide chains fold
Fold spontaneously in aqueous environment
What does the hydrophobic effect drive
Drives formation of hydrophobic core proteins and promotes tertiary structure formation
What are the 3 classes of domain structures
-alpha helical domains
-beta sheet domains
-alpha/beta domains
Characteristics of alpha helical domains
packed together in bundles or ‘coiled -coil’
What do common domains consist of
-pair of helices
-connected by short loop
-packed in anti parallel arrangement
What is a beta sandwich and it’s characteristics
-two beta sheets packed together
-stabilised by ‘fillings’ - hydrophobic side chains
What is the B - barrel and its characteristics
-eight b -strands may form closed ‘barrel’ structure (Chinese finger trap looking like)
Hydrophobic residues orientated towards centre of barrel
What is the Ross man fold
Beta strand and alpha helical repeats
In clonal selection what happens to activated B cells
B cell clone will proliferate and differentiate into antibody secreting cells
What is innate immunity
Rapid but non-specific
What is adaptive immunity
Based on lymphocyte with antigen receptors - immunological memory
What is the epitope
The antigenic determinant and site where antibody binds to on the antigen
What is neutralisation in immunity
Binding of antibodies to epitope on surface of pathogens prevents entry to host cells
What is opsonisation in immunity
The coating of a pathogen with molecules like antibodies and increases efficiency of phagocytosis
What agglutination in immunity
The process of the clumping of pathogens driven by interaction of antibody with antigens and prevents spread of pathogens through the system
What is the complement cascade in immunity
Antibody-antigen complex stimulates binding of Cl => activation of protease that triggers chains of amplification cascade
What is antibody dependant cellular cytotoxicity in immunology
Mechanism where large pathogens are killed by secretion of cytotoxic
What is the stimulation of cytokine release in immunology
IgE antibodies bind to receptors on mast cells and basophils => antigen binding to IgE on these cells stridulate the secretion of cytokines and histamine
What does histamine do
Causes vasodilation and leafiness in blood vessels - its release causes allergic reactions
What are IgE antibodies produced in response to
Response to parasites and environmental allergens e.g pollen, food and drugs
What is the structure of immunoglobulin (Ig)/antibody)
-4 polypeptide chains - two heavy (H) chains
- two light (L) chains
-linked by disulphide bonds
